Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002161
UniProt IDO43189
Primary gene name(s)PHF1
Synonym gene name(s)PCL1
Protein namePHD finger protein 1
Protein functionPolycomb group, PcG that specifically binds histone H3 trimethylated at 'Lys-36', H3K36me3 and recruits the PRC2 complex. Involved in DNA damage response and is recruited at double-strand breaks, DSBs. Acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting the PRC2 complex: it is however unclear whether recruitment of the PRC2 complex to H3K36me3 leads to enhance or inhibit H3K27me3 methylation mediated by the PRC2 complex. According to some reports, PRC2 recruitment by PHF1 promotes H3K27me3 and subsequent gene silencing by inducing spreading of PRC2 and H3K27me3 into H3K36me3 loci, PubMed:18285464 and PubMed:23273982. According to another report, PHF1 recruits the PRC2 complex at double-strand breaks, DSBs and inhibits the activity of PRC2, PubMed:23142980. Regulates p53/TP53 stability and prolonges its turnover: may act by specifically binding to a methylated from of p53/TP53. {ECO:0000269|PubMed:18086877, ECO:0000269|PubMed:18285464, ECO:0000269|PubMed:18385154, ECO:0000269|PubMed:23142980, ECO:0000269|PubMed:23150668, ECO:0000269|PubMed:23273982}.
Subcellular locationNucleus. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Localizes specifically to the promoters of numerous target genes. Localizes to double-strand breaks, DSBs sites following DNA damage. Co-localizes with NEK6 in the centrosome.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: O43189
Gene Ontology
(Biological Process)
Complete annatation
cellular response to DNA damage stimulus [GO:0006974];
covalent chromatin modification [GO:0016569];
negative regulation of gene expression, epigenetic [GO:0045814];
negative regulation of histone H3-K27 methylation [GO:0061086];
positive regulation of histone H3-K27 methylation [GO:0061087];
transcription, DNA-templated [GO:0006351]
Gene Ontology
(Molecular Function)
Complete annatation
methylated histone binding [GO:0035064];
transcription factor activity, sequence-specific DNA binding [GO:0003700];
zinc ion binding [GO:0008270]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
microtubule organizing center [GO:0005815];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
site of double-strand break [GO:0035861]
Protein-protein interaction111271
Phylogenetic treeO43189
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
      Yes - Two siRNA pools inhibit HIV replication and inhibition of Tat-mediated transactivation of the HIV LTR is not observed
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
gene status
Lu et al., J. Virol., 2011
      Folds changes 8h: unknown; Folds changes 16h: unknown; Tested: unknown;
Schoggins JW and Rice CM, Curr. Opin. Virol., 2011
      Targeted viruses: WNV
      Viral life cycle: unknown
      Mechanism related to antiviral activity: unknown
Anti-viral restriction factor Liu et al., Retrovirology, 2011
      unknown (Triplicates)

Gene Expression Profile       top

            Up-regulated;            Down-regulated

For brief introduction to each study, please go to the help page.

Gene expression during HIV latency

(1). Mohammadi et al., PLoS Pathog., 2014

Differentially expressed transcripts (Pairwise) during latency and subsequent viral reactivation using several agents - Primary CD4+ T-cell based model

DMSO: Dimethyl suloxyde (negative control) - 0.0033% final
SAHA: Vorinostat (Histone deacetylase inhibitor) - 0.5 μM
CD3: TCR Stimulation by IL-2+ antiCD3/anti-CD28 antibodies
IL7: Interleukin-7 based stimulation
DISU: Disulfiram (alcohol dehydrogenase inhibitor) - 0.5 μM
AZA: 5-azacytidine (AZA; DNA methylation inhibitor) - 1 μM
Experimental Condition Log2 Fold Change P value Adjusted P value
AZA vs. CD3-1.526712263400495.27614316336855e-063.4774682764728e-05
AZA vs. DISU0.6659592892502510.008880154175886950.235253855970685
AZA vs. IL7-0.5155580853929030.01081719965109660.33968260487704
AZA vs. SAHA0.08615561733920330.7241465530266760.923073348989435
DISU vs. CD32.179169337261528.24205337313089e-091.30779697417447e-07
DISU vs. IL7-1.191269713533373.3619222539194e-060.000359439560126489
DISU vs. SAHA-0.5765611627418060.0499642796925190.279514350128417
DMSO vs. AZA0.01840989069753550.9125550109192471
DMSO vs. CD31.533483978669862.86853792463848e-061.86671809221074e-05
DMSO vs. DISU-0.6493665677104420.008206548493576490.194453908487732
DMSO vs. IL7-0.5265552409089850.003535677412821790.117923830356644
DMSO vs. SAHA0.0629461150289210.7894926239961070.940286000318833
HIV vs. Mock in Activation0.373278570020020.550778556121020.999983755607037
HIV vs. Mock in Latency0.1272969123118910.4401388573681810.999834320637052
IL7 vs. CD31.015686934359350.001808614942360840.00706799404361031
SAHA vs. CD31.58995894883821.21962260963837e-057.4381678378188e-05
SAHA vs. IL70.5992910770337450.01423250713105140.0799928458215767
(2). Iglesias-Ussel et al., J. Virol., 2013

Up and Downregulated transcripts during Latency (Latently infected CD4+ T cells vs Uninfected)- Primary CD4+Tcell based model
Log2 Fold Change P Value
unknown unknown

Gene expression during HIV infection and replication

(1). Imbeault et al., PloS Pathog., 2012

Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells
Experiment type Log2 Fold Change P Value Adjusted P Value
Infected vs. Mock unknown unknown unknown
Infected vs. Bystander unknown unknown unknown
(2). Lefebvre et al., J. Virol., 2011

Transcriptome analysis of T-cell line (Sup T1)
Log2 Fold Change unknown
(3). Li et al., J. Immunol., 2013

Lymphatic tissue
Acute Fold Change Acute P Value Asymt Fold Change Asypt P Value AIDS Fold Change AIDS P Value
2 0.000394482 1.3 0.044517451 1.4 0.15418309
(4). Chang et al., MBio., 2011

Transcriptome analysis of T-cell line (Sup T1)

Derived from Sherrill-Mix et al., BMC Retrovirol., 2015 cross validation
Up-regulated (True) TRUE
(5). Sherrill-Mix et al., BMC Retrovirol., 2015

Deep RNA-seq analysis of primary human T cell infected with low passage HIV isolate HIV89.6 - Primary CD4+ T cell based
Test Status Log2 Fold Change P Value
OK 0.834131 0.000305467
(6). Rotger et al., PLoS Pathog., 2010

Genome-wide mRNA expression of CD4+ T cells from HIV-infected patient
(Genes differentially expressed (at adjusted p<0.01) according to the empirical Bayes approach)
Log2 Fold Change P Value
unknown unknown

Proteomic/Transcriptomics studies indicating differentially expressed genes mediated by HIV

(1). Greenwood et al., Elife, 2016

Activated (CD3/CD28) Primary human CD4+ T cells infected with pNL4-3-dE-EGFP. The table shows the complete (unfiltered) TMT (tandem mass tag)-based proteomic time course dataset
6 h 24 h 48 h 72 h RTi
0.893 1.004 1.212 1.425 1.133
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
unknown unknown unknown unknown unknown unknown unknown
(3). Hyrcza et al., J. Virolo., 2007

Primary human CD4+ and CD8+ T Cells
Affymetrix Prob ID Fold Change In CD8? Category
unknown unknown unknown unknown

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
2E5P NMR - A=29-83.
2M0O NMR - A=6-83.
4HCZ X-ray 1.8Å A/B=28-85.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

HIV Partner Interaction Type PubMed
HIV-1 virus replication regulated by expression of human gene 18976975

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found